Man pages for R453Plus1Toolbox
A package for importing and analyzing data from Roche's Genome Sequencer System

alignShortReadsExact alignment of DNA sequences against a reference
AnnotatedVariants-classClass "AnnotatedVariants"
annotateVariantsAdds genomic information to variants
assayDataAmpAccess the amplicon data of an AVASet.
ava2vcfConvert an AVASet object into a VCF object
AVASetCreating an AVASet
AVASet-classClass to contain Amplicon Variant Analyzer Output
avaSetExampleAmplicon Variant Analyzer data import
avaSetFilteredAmplicon Variant Analyzer data import
avaSetFiltered_annotAVASet variant annotations
baseFrequencyAbsolute And Relative Frequency Of The Four Bases.
baseQualityHistPlot A Histogram Of The Base Qualities.
baseQualityStatsStatistics Of Base Quality
breakpointsPutative breakpoints of chimeric reads
Breakpoints-classClass "Breakpoints"
calculateTiTvCalculate transition transversion ratio
captureArrayCustom capture array design
complexity.dustSequence Complexity Using The DUST Algorithm
complexity.entropySequence Complexity Using The Shannon-Wiener Algorithm
convertCigarBasic functions for CIGAR strings
coverageOnTargetComputes the coverage restricted to the target region.
demultiplexReadsPerforms MID/Multiplex filtering
detectBreakpointsClustering and consensus breakpoint detection for chimeric...
dinucleotideOddsRatioDinucleotide Odds Ratio
fDataAmpAccess the amplicon data of an AVASet.
featureDataAmpAccess the amplicon data of an AVASet
filterChimericReadsExtract chimeric reads and apply filtering steps to remove...
flowgramBarplotCreate A Barplot Of The Flow Intensities
gcContentCalculate The Overall GC-Content
gcContentHistGC-Content Histogram
gcPerPositionGC-Content Per Position
genomeSequencerMIDsRetrieve GS multiplex sequences
getAlignedReadsImport reads from an Amplicon Variant Analyzer project
getAminoAbbrGet amino acid abbreviations
getVariantPercentagesVariant coverage
homopolymerHistCreate A Histogram Of The Homopolymer Stretches
htmlReportHTML-Report Builder for the AVASet and MapperSet
MapperSetCreating a MapperSet
MapperSet-classClass to Contain GS Reference Mapper Output
mapperSetExampleGS Reference Mapper data import
mergeBreakpointsIdentify and merge related breakpoints caused by the same...
mutationInfoExample data for 'plotVariants'
nucleotideChartsNucleotide Charts
plotAmpliconCoverageCreates a plot visualizing the number of reads per amplicon
plotChimericReadsPlots chimeric reads
plotVariantsPlots variant positions
plotVariationFrequencyCreate an AVA style variation frequency plot
positionQualityBoxplotBoxplot Of The Quality For Each Position
qualityReportSFFFunction To Create A Quality Report In PDF Format
readLengthHistHistogram Of The Read Lengths
readLengthStatsStatistics For The Read Lengths
readSFFFunction To Read In Roche's .sff Files
readsOnTargetCheck for each read whether it aligns within the given...
referenceSequencesAccess the reference sequences of an AVASet
regionsExample data for 'plotVariants'
removeLinkerRemove linker sequences located at the start of short reads
sequenceCaptureLinkersRetrieve NimbleGen's sequence capture linkers
sequenceQualityHistA Histogram Of The Sequence Qualities
setVariantFilterFilters output of variant information
sff2fastqWrite A SFFContainer Object To A FASTQ File
SFFContainer-classClass '"SFFContainer"'
SFFRead-classClass '"SFFRead"'
variantsExample data for 'plotVariants'
writeSFFFunction To Write Files In Roche's .sff Format
R453Plus1Toolbox documentation built on Nov. 8, 2020, 5:59 p.m.